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Posted to issues@spark.apache.org by "Furcy Pin (JIRA)" <ji...@apache.org> on 2018/02/19 17:47:00 UTC
[jira] [Commented] (SPARK-17430) Spark task Hangs after OOM while
DAG scheduler tries to serialize a task
[ https://issues.apache.org/jira/browse/SPARK-17430?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16369367#comment-16369367 ]
Furcy Pin commented on SPARK-17430:
-----------------------------------
Same problem here in spark 2.2.1
The job hangs forever, the GUI is still responsive but no task advances and the executors are still reserved.
This can be really annoying as it create zombie jobs eating cluster resources for nothing until they are killed manually.
The StackTrace in the driver logs gave this error:
{code:java}
WARN util.Utils: Suppressing exception in finally: Java heap space
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3236)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:118)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:253)
at java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:211)
at java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:145)
at java.io.ObjectOutputStream$BlockDataOutputStream.writeBlockHeader(ObjectOutputStream.java:1894)
at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1875)
at java.io.ObjectOutputStream$BlockDataOutputStream.flush(ObjectOutputStream.java:1822)
at java.io.ObjectOutputStream.flush(ObjectOutputStream.java:719)
at java.io.ObjectOutputStream.close(ObjectOutputStream.java:740)
at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$2.apply$mcV$sp(MapOutputTracker.scala:620)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1346)
at org.apache.spark.MapOutputTracker$.serializeMapStatuses(MapOutputTracker.scala:619)
at org.apache.spark.MapOutputTrackerMaster.getSerializedMapOutputStatuses(MapOutputTracker.scala:562)
at org.apache.spark.scheduler.DAGScheduler.createShuffleMapStage(DAGScheduler.scala:341)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$getOrCreateShuffleMapStage$1.apply(DAGScheduler.scala:312)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$getOrCreateShuffleMapStage$1.apply(DAGScheduler.scala:305)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.mutable.Stack.foreach(Stack.scala:169)
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$getOrCreateShuffleMapStage(DAGScheduler.scala:305)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$getOrCreateParentStages$1.apply(DAGScheduler.scala:381)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$getOrCreateParentStages$1.apply(DAGScheduler.scala:380)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.mutable.HashSet.foreach(HashSet.scala:79)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
at scala.collection.mutable.AbstractSet.scala$collection$SetLike$$super$map(Set.scala:45)
at scala.collection.SetLike$class.map(SetLike.scala:93)
Exception in thread "dag-scheduler-event-loop" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3236)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:118)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:253)
at java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:211)
at java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:145)
at java.io.ObjectOutputStream$BlockDataOutputStream.writeBlockHeader(ObjectOutputStream.java:1894)
at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1875)
at java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1786)
at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1189)
at java.io.ObjectOutputStream.writeArray(ObjectOutputStream.java:1378)
at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1174)
at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348)
at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply$mcV$sp(MapOutputTracker.scala:617)
at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply(MapOutputTracker.scala:616)
at org.apache.spark.MapOutputTracker$$anonfun$serializeMapStatuses$1.apply(MapOutputTracker.scala:616)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1337)
at org.apache.spark.MapOutputTracker$.serializeMapStatuses(MapOutputTracker.scala:619)
at org.apache.spark.MapOutputTrackerMaster.getSerializedMapOutputStatuses(MapOutputTracker.scala:562)
at org.apache.spark.scheduler.DAGScheduler.createShuffleMapStage(DAGScheduler.scala:341)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$getOrCreateShuffleMapStage$1.apply(DAGScheduler.scala:312)
at org.apac{code}
> Spark task Hangs after OOM while DAG scheduler tries to serialize a task
> ------------------------------------------------------------------------
>
> Key: SPARK-17430
> URL: https://issues.apache.org/jira/browse/SPARK-17430
> Project: Spark
> Issue Type: Bug
> Components: Scheduler
> Affects Versions: 1.6.2
> Reporter: Mikhail Galanin
> Priority: Major
> Attachments: abort-task-on-oom-in-dag-scheduler.patch
>
>
> Hi here,
> We're running Spark under Hadoop 2.7.1 Yarn and faced a problem.
> The problem is that sometimes an exception raises inside JavaSerializer (see the stacktrace below). The exception isn't a problem itself but after it happens, the task hangs. It's shown as "running" in the Hadoop task list but no one worker is executing task, no more records appear in Spark job log until somebody kills it.
> We have fixed the issue by patching Spark code (catch OOM in submitMissingTasks()) but it looks like OOM error is deliberately ignored so probably there should be a better solution.
> {noformat}
> Exception in thread "dag-scheduler-event-loop" java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOf(Arrays.java:3332)
> at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
> at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121)
> at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:421)
> at java.lang.StringBuilder.append(StringBuilder.java:136)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1421)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1548)
> at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1509)
> at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1432)
> at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1178)
> at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348)
> at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:44)
> at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:101)
> at org.apache.spark.scheduler.DAGScheduler.submitMissingTasks(DAGScheduler.scala:1003)
> at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$submitStage(DAGScheduler.scala:921)
> at org.apache.spark.scheduler.DAGScheduler.handleJobSubmitted(DAGScheduler.scala:861)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1607)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1599)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1588)
> {noformat}
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